Musa scored in the 65th minute but Plzen replied with two goals in the 76th and in the 90th minutes to get their only win in the group. CSKA had beaten Plzen 3-2 in their first meeting in October.
It was Musa’s first goal in 20 games, as he last scored in the league on August 30 against Amkar Perm.
Musa headed the Russian champions into the lead off a cross by Keisuke Honda before Daniel Kolar restored parity. Tomas Wagner then scored the winner for the Czech Republic side very late after Vitinho had substituted Musa.Though they lost, CSKA finished third in Group D, which Bayern Munich won. The Russian side will now go into the Europa League.